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  "Package": "spleenrbc",
  "Title": "The role of the spleen in red blood cell loss due to malaria",
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  "Authors@R": "c(\nperson(\"Saber\", \"Dini\", email = \"saber.dini@unimelb.edu.au\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-4613-3672\")),\nperson(\"Ali\", \"Haghiri\", email = \"haghiri.a@unimelb.edu.au\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-6008-3165\")),\nperson(\"Robert\", \"Moss\", email = \"rgmoss@unimelb.edu.au\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-4568-2012\")))",
  "Description": "A mathematical model of red blood cell (RBC) dynamics in a\nmalaria infection, which includes the spleen as a separate\nmodel compartment that can retain large amounts of infected and\nuninfected RBCs.",
  "License": "MIT + file LICENSE",
  "URL": "https://gitlab.unimelb.edu.au/rgmoss/malaria-spleen-rbc-loss/",
  "BugReports": "https://gitlab.unimelb.edu.au/rgmoss/malaria-spleen-rbc-loss/issues",
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  "Repository": "https://robmoss.r-universe.dev",
  "Date/Publication": "2026-02-19 06:37:01 UTC",
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  "Author": "Saber Dini [aut] (ORCID: <https://orcid.org/0000-0002-4613-3672>),\nAli Haghiri [aut] (ORCID: <https://orcid.org/0000-0002-6008-3165>),\nRobert Moss [aut, cre] (ORCID: <https://orcid.org/0000-0002-4568-2012>)",
  "Maintainer": "Robert Moss <rgmoss@unimelb.edu.au>",
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    "alpha_c",
    "alpha_r",
    "baseline_parameters",
    "beta",
    "calculate_irbc_ratio",
    "calculate_steady_state_outputs",
    "calculate_urbc_loss_ratio",
    "calculate_urbc_ratio",
    "define_derived_parameters",
    "delta_i",
    "delta_i_fold",
    "delta_i_prime",
    "delta_u",
    "delta_u_fold",
    "delta_u_prime",
    "erythropoiesis",
    "individual_results",
    "infection_flows_and_loss",
    "initial_spleenrbc_state",
    "lambda_i",
    "lambda_u",
    "prepare_spleenrbc_snapshot",
    "qlunif",
    "rbc_counts_to_haemoglobin",
    "resolve_negative_rbcs",
    "retic_steady_state",
    "reticulocyte_prod",
    "rho",
    "rho_release_age",
    "run_spleenrbc",
    "run_spleenrbc_model",
    "sample_parameters",
    "step_spleenrbc_model",
    "uncertainty_distributions",
    "uncertainty_intervals",
    "zeta"
  ],
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    {
      "name": "hhs_asymp",
      "title": "Red blood cell counts collected from asymptomatic Papuans who reported no fever within the preceding 24 hours (708 uninfected, 50 Pf infections, 45 Pv infections) in a cross-sectional household survey conducted in southern Papua, Indonesia.",
      "object": "hhs_asymp",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "species",
        "total_rbc"
      ],
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      "table": true,
      "tojson": true
    },
    {
      "name": "parameters_pf",
      "title": "Pf parameter values for each scenario.",
      "object": "parameters_pf",
      "class": [
        "data.frame"
      ],
      "fields": [
        "name",
        "baseline"
      ],
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      "table": true,
      "tojson": true
    },
    {
      "name": "parameters_pv",
      "title": "Pv parameter values for each scenario.",
      "object": "parameters_pv",
      "class": [
        "data.frame"
      ],
      "fields": [
        "name",
        "baseline"
      ],
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      "table": true,
      "tojson": true
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    {
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      "title": "The red blood cell count at homeostasis.",
      "object": "rbc_steady_state",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
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      "name": "splenectomised",
      "title": "Uninfected and infected RBC counts in the circulation and spleen of 15 asymptomatic adults in Papua, Indonesia (9 Pf infections, 6 Pv infections) who underwent splenectomy, mostly due to trauma.",
      "object": "splenectomised",
      "class": [
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        "tbl",
        "data.frame"
      ],
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        "infection",
        "irbc_peri",
        "irbc_spleen",
        "urbc_peri",
        "urbc_spleen"
      ],
      "rows": 17,
      "table": true,
      "tojson": true
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  "_help": [
    {
      "page": "alpha_c",
      "title": "Age-structured parasite multiplication rates (the number of released merozoites that successfully invade uRBCS of age 'a') in the circulation.",
      "topics": [
        "alpha_c"
      ]
    },
    {
      "page": "alpha_r",
      "title": "Age-structured parasite multiplication rates (the number of released merozoites that successfully invade uRBCS of age 'a') in the spleen.",
      "topics": [
        "alpha_r"
      ]
    },
    {
      "page": "baseline_parameters",
      "title": "Return the baseline parameter values, including all derived parameters.",
      "topics": [
        "baseline_parameters"
      ]
    },
    {
      "page": "beta",
      "title": "Age-dependent merozoite preference for uninfected RBCs.",
      "topics": [
        "beta"
      ]
    },
    {
      "page": "calculate_irbc_ratio",
      "title": "Calculate the ratio of (a) the fraction of RBCs in the spleen that are infected; to (b) the fraction of RBCs in the circulation that are infected.",
      "topics": [
        "calculate_irbc_ratio"
      ]
    },
    {
      "page": "calculate_steady_state_outputs",
      "title": "Calculate steady-state values for high-level model outputs.",
      "topics": [
        "calculate_steady_state_outputs"
      ]
    },
    {
      "page": "calculate_urbc_loss_ratio",
      "title": "Calculate the ratio of (a) the unparasitised RBC loss due to malaria (additional uRBC retention in the spleen); to (b) the parasitised RBC loss due to RBC infection.",
      "topics": [
        "calculate_urbc_loss_ratio"
      ]
    },
    {
      "page": "calculate_urbc_ratio",
      "title": "Calculate the ratio of (a) the fraction of uRBCs retained in the spleen at time 't'; to (b) the fraction of uRBCs retained in the spleen at homeostasis.",
      "topics": [
        "calculate_urbc_ratio"
      ]
    },
    {
      "page": "define_derived_parameters",
      "title": "Define parameters whose values are derived from other parameters.",
      "topics": [
        "define_derived_parameters"
      ]
    },
    {
      "page": "delta_i",
      "title": "Rate of infected RBC removal from the circulation into the spleen.",
      "topics": [
        "delta_i"
      ]
    },
    {
      "page": "delta_i_fold",
      "title": "Increase in infected RBC removal into the spleen due to RBC congestion.",
      "topics": [
        "delta_i_fold"
      ]
    },
    {
      "page": "delta_i_prime",
      "title": "Rate of infected RBC reentry into the circulation from the spleen.",
      "topics": [
        "delta_i_prime"
      ]
    },
    {
      "page": "delta_u",
      "title": "Rate of uninfected RBC removal from the circulation into the spleen.",
      "topics": [
        "delta_u"
      ]
    },
    {
      "page": "delta_u_fold",
      "title": "Increase in uninfected RBC removal into the spleen due to RBC congestion.",
      "topics": [
        "delta_u_fold"
      ]
    },
    {
      "page": "delta_u_prime",
      "title": "Rate of uninfected RBC reentry into the circulation from the spleen.",
      "topics": [
        "delta_u_prime"
      ]
    },
    {
      "page": "erythropoiesis",
      "title": "Rate of RBC production.",
      "topics": [
        "erythropoiesis"
      ]
    },
    {
      "page": "hhs_asymp",
      "title": "Red blood cell counts collected from asymptomatic Papuans who reported no fever within the preceding 24 hours (708 uninfected, 50 Pf infections, 45 Pv infections) in a cross-sectional household survey conducted in southern Papua, Indonesia.",
      "topics": [
        "hhs_asymp"
      ]
    },
    {
      "page": "individual_results",
      "title": "Record key outputs for a single scenario.",
      "topics": [
        "individual_results"
      ]
    },
    {
      "page": "infection_flows_and_loss",
      "title": "Calculate quantities related to uRBC infection and retention in the spleen due to malaria infection.",
      "topics": [
        "infection_flows_and_loss"
      ]
    },
    {
      "page": "initial_spleenrbc_state",
      "title": "Construct the initial model state.",
      "topics": [
        "initial_spleenrbc_state"
      ]
    },
    {
      "page": "lambda_i",
      "title": "Phagocytosis rate of infected RBCs in the spleen.",
      "topics": [
        "lambda_i"
      ]
    },
    {
      "page": "lambda_u",
      "title": "Phagocytosis rate of uninfected RBCs in the spleen.",
      "topics": [
        "lambda_u"
      ]
    },
    {
      "page": "parameters_pf",
      "title": "Pf parameter values for each scenario.",
      "topics": [
        "parameters_pf"
      ]
    },
    {
      "page": "parameters_pv",
      "title": "Pv parameter values for each scenario.",
      "topics": [
        "parameters_pv"
      ]
    },
    {
      "page": "prepare_spleenrbc_snapshot",
      "title": "Construct a list that will record the model state over time.",
      "topics": [
        "prepare_spleenrbc_snapshot"
      ]
    },
    {
      "page": "qlunif",
      "title": "Quantile function for the log-uniform distribution.",
      "topics": [
        "qlunif"
      ]
    },
    {
      "page": "rbc_counts_to_haemoglobin",
      "title": "Convert red blood cell counts into haemoglobin (g/dL).",
      "topics": [
        "rbc_counts_to_haemoglobin"
      ]
    },
    {
      "page": "rbc_steady_state",
      "title": "The red blood cell count at homeostasis.",
      "topics": [
        "rbc_steady_state"
      ]
    },
    {
      "page": "resolve_negative_rbcs",
      "title": "Subtract negative U values from other (positive) U values.",
      "topics": [
        "resolve_negative_rbcs"
      ]
    },
    {
      "page": "retic_steady_state",
      "title": "The reticulocyte production rate at homeostasis.",
      "topics": [
        "retic_steady_state"
      ]
    },
    {
      "page": "reticulocyte_prod",
      "title": "The reticulocyte production rate for the given normoblast population.",
      "topics": [
        "reticulocyte_prod"
      ]
    },
    {
      "page": "rho",
      "title": "Age-structured release rate of reticulocytes from the bone marrow into the circulation.",
      "topics": [
        "rho"
      ]
    },
    {
      "page": "rho_release_age",
      "title": "The minimum age at which reticulocytes are released from the bone marrow into the circulation.",
      "topics": [
        "rho_release_age"
      ]
    },
    {
      "page": "run_spleenrbc",
      "title": "Run model scenarios.",
      "topics": [
        "run_spleenrbc"
      ]
    },
    {
      "page": "run_spleenrbc_model",
      "title": "Run a single scenario and return the model state history.",
      "topics": [
        "run_spleenrbc_model"
      ]
    },
    {
      "page": "sample_parameters",
      "title": "Create parameter samples for each scenario.",
      "topics": [
        "sample_parameters"
      ]
    },
    {
      "page": "splenectomised",
      "title": "Uninfected and infected RBC counts in the circulation and spleen of 15 asymptomatic adults in Papua, Indonesia (9 Pf infections, 6 Pv infections) who underwent splenectomy, mostly due to trauma.",
      "topics": [
        "splenectomised"
      ]
    },
    {
      "page": "step_spleenrbc_model",
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      "topics": [
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      "title": "Define uncertainty distributions for each parameter.",
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      "title": "Calculate uncertainty intervals for each column, except for \"time\" and \"scenario\".",
      "topics": [
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      ]
    },
    {
      "page": "zeta",
      "title": "Age-structured rate of RBC sequestration into the microvasculature.",
      "topics": [
        "zeta"
      ]
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